I have a 260 with a 9.9 Honda as well. The motor is 2006. The boat had a Nissan motor when I bought it.
I believe it has the original factory cables. They were quite smouth on the Nissan. I installed the Honda motor myself.
The throttle is fine on the Honda but the shift is very stiff, I think it is the detent on the Honda shift linkage. There is a shifter shaft inside the case, across the front of the motor that rotates, there is tiny arm that presses against this shaft to provide the detents. That is what appears to be causing the hard shift on my motor. I removed one of the springs,(mine had 2) it is a flat piece of metal, and it improved quite a bit, I intend to try and release more of the pressure, perhaps using a shim - a washer might do it. I used it the way it is this summer but I think it is going to lead to premature failure of the cable if the pressure is not reduced. I don't know if this has anything to do with your situation.
I am also looking for a good way to mount a small outboard motor on the back of the boat. I have seen pictures of a bracket behind the helm seat so the motor is hanging out behind the helm, but not enough detail in the shot, it was a boat that was for sale. I include the picture below, maybe someone has seen this boat and can add some details, it has a full dodger/cockpit enclosure as well. If you come up with an elegant solution please post a picture. I am heading south with the boat in January and would like to solve this before I leave.
good luck, Bob